Contacts of the helix formed by residues 345 - 350 (chain A) in PDB entry 2XGZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A ASP* 3.1 23.8 + - - +
321A ARG* 3.2 5.1 - - - +
325A THR* 2.9 16.1 + - - -
343A LEU* 3.6 20.0 - - + +
344A LEU* 1.3 74.3 - - - +
346A VAL* 1.3 66.5 + - - +
347A ASN 3.1 1.6 - - - -
348A GLN* 2.9 50.0 + - + +
372A SER* 3.8 18.2 - - - +
373A HIS 3.7 13.2 - - - +
374A ARG* 3.6 29.0 - - - +
1440A PEP 2.8 37.7 + - - -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 5.2 9.0 - - + -
111A LEU* 3.9 28.0 - - + +
115A LEU* 4.6 13.9 - - + -
344A LEU* 4.0 2.9 + - + +
345A LYS* 1.3 71.3 - - - +
347A ASN* 1.3 60.7 + - + +
349A ILE* 3.3 6.4 + - - +
350A GLY* 2.9 26.2 + - - -
351A THR 5.2 0.2 - - - +
352A LEU* 4.7 10.1 - - + -
355A SER* 3.3 28.6 + - - +
372A SER 5.3 1.0 + - - +
382A PHE* 4.9 3.4 - - + -
383A ILE* 5.1 13.4 - - + +
386A LEU* 3.8 28.7 - - + -
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Residues in contact with ASN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.5 5.8 - - + +
35A PRO* 3.2 34.0 + - + +
36A SER* 4.3 5.3 - - - +
37A GLY 4.7 0.6 - - - +
44A GLU* 4.8 3.0 + - - +
45A ALA* 4.4 5.9 - - - +
47A GLU* 4.6 11.3 + - - +
107A ALA* 4.4 15.4 - - + +
108A ASN* 6.2 0.4 - - - +
111A LEU* 3.5 23.3 - - + -
345A LYS* 3.1 2.1 - - - +
346A VAL* 1.3 76.8 - - - +
348A GLN* 1.3 63.5 + - - +
349A ILE 3.2 2.4 + - - -
350A GLY* 4.1 6.0 + - - +
374A ARG* 2.9 46.2 + - - +
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Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS 4.7 0.9 - - - +
44A GLU* 3.2 43.1 + - + -
45A ALA 2.9 24.5 + - - -
320A ASP* 2.9 28.4 + - - +
321A ARG* 4.3 2.2 - - - +
324A VAL* 3.3 39.4 - - - +
325A THR* 2.8 19.1 + - - +
326A ASN* 5.9 0.2 + - - -
343A LEU 4.2 2.3 - - - +
345A LYS* 2.9 30.8 + - + +
347A ASN* 1.3 78.5 + - - +
349A ILE* 1.3 60.2 + - - +
374A ARG* 3.5 9.2 - - - +
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 3.6 9.3 - - + +
102A LYS* 2.9 30.8 + - - +
325A THR* 3.3 27.6 - - + +
326A ASN* 3.7 37.7 - - + +
327A PRO* 4.5 3.1 - - + -
346A VAL 3.5 2.0 - - - +
348A GLN* 1.3 83.8 - - - +
350A GLY* 1.3 59.8 + - - +
351A THR 3.6 9.2 - - - +
354A GLU* 3.6 29.8 - - + +
355A SER* 3.3 31.9 - - - +
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 4.0 11.4 - - - -
107A ALA* 4.2 13.7 - - - -
110A ILE* 3.4 3.3 - - - +
111A LEU* 3.3 37.5 + - - -
346A VAL 2.9 13.3 + - - -
347A ASN* 4.1 2.6 - - - -
348A GLN 3.9 0.4 - - - -
349A ILE* 1.3 77.1 - - - +
351A THR* 1.3 66.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il